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Version history

• v1.7.1

  03.12.2024

  • Fixes the NCBI dataset zip loading behavior to avoid that the progress dialog is still shown when no file is selected.
• v1.7.0

  03.12.2024

  • Adds support from loading NCBI dataset zip files.
• v1.6.1

  12.11.2024

  • Fixes the NCBI Rename operation to work with the new "Datasets" web interface.
• v1.6.0

  23.11.2023

  • Adds a Command-Line Interface (CLI) for all operations.
  • Creation of new distributions for APT (Advanced Package Tool), used in Debian-based distributions like Ubuntu or Kubuntu, RPM (Red Hat Package Manager), used in Fedora or CentOS, among others, and Snap.
  • Fixes a bug when filtering by reference sequence size difference from an external file.
  • In addition, the SEDA pipelines with Compi project provides a framework for easily creating pipelines made up of SEDA commands using Compi.
• v1.5.1

  16.05.2023

  • Fixes the PfamScan operation that was not working due to changes in the web service.
  • Fixes a bug in the PfamScan operation that was causing the expectation value was not submitted in the query.
• v1.5.0

  27.06.2022

  • Adds support for running the CGA (Conserved Genome Annotation) Pipeline as a new Gene annotation operation.
• v1.4.0

  26.05.2021

  • Fixes the Splign/Compart protocol to properly retrieve the FASTA sequences from the Splign/Compart annotations. So far, we were creating a bidirectional genome (the original genome plus its reverse-complement) but we realized that Splign/Compart is able to annotate in both strands and therefore such bidirectional genome is no longer needed. After removing this, the way that the FASTA sequences are extracted from the annotations varies depending on the query/subject start/end coordinates. This is described in the corresponding section of the manual.
• v1.3.2

  10.05.2021

  • Fixes a bug when running BLAST operations using Docker. The bug was only affecting to BLAST commands execution in Docker that require protein databases (e.g. blastp) and use an alias (i.e. "query against all databases" was used).
• v1.3.1

  14.04.2021

  • Fixes an important bug in the ProSplign/ProCompart pipeline. The tblastn output must be sorted by subject and query and so far it was not being sorted properly. This commit fixes this behavior and now the output is sorted properly by subject and query as the procompart tool requires.
• v1.3.0

  27.11.2020

  • Fixes unstable Splign/Compart behavior.
  • Allows importing patterns from FASTA files.
  • Add a new consensus sequence mode.
• v1.2.2

  18.10.2020

  • Update junit from 4.12 to 4.13.1.
• v1.2.1

  18.10.2020

  • Reduces RAM memory usage when writing FASTA files.
• v1.2.0

  04.09.2020

  • Add NCBI BLAST and UniProt BLAST operations to run BLAST queries using the NCBI and UniProt web servers respectively.
  • Add PfamScan plugin with a new operation to search and annotate sequences against the Pfam-A HMM library using the EMBL-EBI web service.
  • Parallelize the "BLAST: two-way ortholog identification" operation.
  • Update manual to include step-by-step execution guides of three protocols.
  • Show operation elapsed time when finished.
  • Capture out of memory errors to show a warning message to users.
  • Minor fixes.
• v1.1.0

  16.04.2020

  • Add Reverse Complement plugin.
  • Add Trim Alignment plugin.
  • Add Remove Stop Codons plugin.
  • Add support for reading and writing gzip compressed files.
  • Add an auto-detect encoding mode to support FASTA files containing special characters.
  • Add support for saving and loading the configuration of the operations.
  • Add NCBI genetic codes for sequence translation.
  • Improve both in-memory and in-disk FASTA files processing.
  • Minor fixes.
• v1.0.3

  18.02.2020

  • Update license headers to '2017 - 2020'.
• v1.0.2

  18.02.2020

  • Fix sequence filtering by starting codons to process nucleotide sequences containing ambiguity codes.
• v1.0.1

  10.02.2020

  • Fix sequence filtering by starting codons to process sequences with sizes that are not multiples of 3.
• v1.0.0

  03.12.2019

  • Add Splign/Compart plugin with an operation for gene annotation.
  • Add bedtools plugin.
  • Add ProSplign/ProCompart plugin with an operation for gene annotation.
  • Add GetORF plugin with an operation for gene annotation.
  • Add SAPP plugin with an operation for gene annotation using Augustus.
  • Add developers section to the manual.
  • Allow adding removed isoform headers to the selected isoform header.
  • Allow setting a a random seed in the split sequences operations
  • Change the operation selection interface.
  • Add table header tooltips with statistics.
  • Add file filters when selecting input files.
  • Fix reverse complement and translate functions to deal with lower case characters.
  • Fix isoforms list directory selection.
  • Minor fixes.
• v0.5.7

  19.05.2019

  • Fix sequence translation to preserve alignment gaps (i.e. a triplet of gaps is translated into a single gap).
• v0.5.6

  08.05.2019

  • Fix a bug when loading empty sequence files. This way, operations like BLAST work properly when empty sequence files are produced (e.g. there are no BLAST hits).
• v0.5.5

  03.05.2019

  • Fix the Docker image by removing the Java 8 installation in the Docker image since it is not necessary to run SEDA.
• v0.5.4

  03.05.2019

  • Fix the Multipart header mode of the Rename header operation so that the order of the fields is preserved in the new header.
• v0.5.3

  18.02.2019

  • Fix the BLAST operations to properly check whether the selected BLAST binaries mode is valid or not.
• v0.5.2

  18.02.2019

  • Fix the Clustal Omega operation so that it is executed correctly when the Clustal Omega binary is in the system path.
• v0.5.1

  18.02.2019

  • Fix the two-way BLAST ortholog identification operation so that the BLAST binaries selection is not shown in the Docker image.
• v0.5.0

  10.12.2018

  • Add support to run external software (Clustal Omega and BLAST) using Docker images.
  • Add an operation to compare datasets (i.e. make all the possible pairwise comparisons on the input files)
• v0.4.2

  10.10.2018

  • Fix the SEDA Docker image so that it uses the latest release.
• v0.4.1

  10.10.2018

  • Fix the NCBI Rename operation that was failing when adding taxonomy information.
• v0.4.0

  04.09.2018

  • Allow sequence concatenation based on regular expressions.
  • Fix line breaks preservation in Windows environments.
• v0.3.0

  17.08.2018

  • Add remove isoforms operation.
  • Add Clustal Omega plugin with alignment operation.
  • Add regular expression split operation.
  • Minor bugfixes.
  • GUI improvements.
• v0.2.3

  4.07.2018

  • Fix a bug when reformating a file that caused incorrect end of line characters.
• v0.2.2

  11.06.2018

  • Fix a bug when applying the remove by size difference filter.
• v0.2.1

  25.05.2018

  • Fix Windows and Mac OS X installers.
• v0.2.0

  02.05.2018

  • Add two-way BLAST ortholog identification operation.
  • Create online Read The Docs manual.
• v0.1.2

  02.04.2018

  • Fix a bug when creating consensus the consensus sequence of nucleotide sequences.
• v0.1.1

  23.03.2018

  • Fix a bug when importing patterns into the pattern filtering operation.
• v0.1.0

  12.03.2018

  • First public release of SEDA.